Preheat oven to 350°F (175°C) and line a muffin tin with liners.
Whisk flour, baking powder, baking soda, salt, and spices in a bowl.
Beat butter and sugar until creamy, then add eggs one at a time.
Mix in pumpkin puree, milk, and vanilla until smooth.
Fold dry ingredients into wet ingredients until just combined.
In a small bowl, beat cream cheese, sugar, egg yolk, and vanilla for filling.
Fill muffin cups halfway with pumpkin batter, add a teaspoon of cream cheese filling, then top with remaining batter.
Swirl gently with a toothpick for a marbled effect.
Bake for 22–25 minutes or until a toothpick comes out clean.
Let muffins cool in the pan for 5 minutes, then transfer to a wire rack.